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2D–5D software for visualization, processing and analysis of microscopy images serving life sciences

Thermo Scientific Amira Software is a powerful, comprehensive, and versatile software solution for visualizing, analyzing and understanding life science and biomedical research images from many image modalities, including Optical and Electron Microscopy, CT, MRI and other imaging modalities. 

With incredible speed and flexibility, Amira Software supports advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology to tissue imaging, neuroscience, anatomical imaging and bioengineering. 

Amira Software harnesses the power of artificial intelligence to provide a broad spectrum of data visualization, processing, and analysis capabilities for 3D image data, including time series and multi-channel datasets. Its advanced features enable life science and biomedical researchers to extract valuable insights from their data, regardless of the modality or scale.

Imaging data

Amira Software workflow

Processing

Amira Software workflow

Visualization

Amira Software workflow

Analysis

Amira Software workflow
Customization

Confidence

Thanks to powerful segmentation and image processing capabilities and workflows, and after 20+ years of collaboration with the scientific community and thousands of researchers, it has been now proven that our digital imaging-based workflows provide reliable answers to biomedical and life science research.

Customization

Customization

Because your needs are unique and keep evolving, our software solutions are fully flexible and open to customization. Thanks to our scripting interface (Python, TCL), bridge with MATLAB, and our programming API, you can expand our software solution and integrate your own IP (Intellectual Property). And, if needed, our professional service team can help you design unique solutions tailored to your needs.

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Support

Thanks to our dedicated professional support team, you get access to our top experts to ensure that no question is left unanswered. And with our training, consulting options, and ever-expanding collection of tutorials and how-to’s, you can reduce your learning curve and focus on getting the answers you are pursuing.

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Automation

Thanks to our automation capabilities, and with the addition of our always expanding online repository of add-ons (Xtra Gallery), you can encapsulate repeatable workflows into easy-to-reproduce recipes. With the addition of artificial intelligence, analysis can be performed by non-image processing experts, allowing them to save time on complex analysis while ensuring results consistency.

Applications

Insight from your peers

Explore industry-leading insights and research that can support your lab workflow. Amira Software can empower your lab with a cutting-edge, comprehensive imaging data analysis toolbox.

Helping scientists answer questions that enable breakthrough discoveries in life sciences, materials science, and industry.

Amira Software Supports Mitochondria Research at Vanderbilt University
Read more
Correlative Microscopy: Using Amira Software to Understand the Spread of Cancer
Read more
Amira Software Accelerates Veterinary Research with 3D Visualization and Analysis
Read more
Molecular Clarity—Discovering What’s Possible with Cryo-Electron Tomography
Read more
Cryo-Electron Tomography and 3D Software Advances Coronavirus Research
Read more

 

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Techniques

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

 

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

 

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

 

High Content Screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality

Learn more

 

Multi-channel and time-series visualization

With Amira Software’s new Xplore5D extension, life scientists can easily visualize, correlate, and process large multi-channel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 

Filament tracing

With Amira Software, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam data. In addition, Amira Software enables you to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

 
Correlative imaging

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

 
Membrane detection

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

 
Cell detection

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

 
High Content Screening

High Content Screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality

Learn more

 
Multi-channel and time-series visualization

Multi-channel and time-series visualization

With Amira Software’s new Xplore5D extension, life scientists can easily visualize, correlate, and process large multi-channel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 
Filament tracing

Filament tracing

With Amira Software, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam data. In addition, Amira Software enables you to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

 

Services

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Introductory training

Shorten your learning curve and maximize your investment with this introductory training specifically designed for new users of Amira, Avizo and PerGeos Software.

The course consists of a lecture with hands-on sessions. The training material highlights the basic features and functionalities of Amira, Avizo and PerGeos Software.

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Advanced training

Maximize your investment and reduce your time-to-results with this advanced training specifically designed for existing users of Amira, Avizo and PerGeos Software.

The course consists of a lecture with hands-on sessions. The training material highlights advanced features and functionalities of Amira, Avizo and PerGeos Software.

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Custom development

With over 25 years of experience in 3D and image processing and hundreds of custom projects delivered to organizations small and large, Thermo Fisher Scientific can provide you with a solution tailored to fit your specific needs.

We can customize and expand our software solutions at various levels.

Learn more

Testimonials

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    Dr. Antentor Hinton Jr, has made extensive use of Amira Software as part of his lab’s work in mitochondrial research.

    "Amira Software is crucial for visualizing SBF-SEM (serial block-face SEM) and FIB-SEM images, so we can analyze the 3D morphology of organelles."

    Dr. Antentor Hinton Jr
    Department of Molecular Physiology and Biophysics, Vanderbilt University

     

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      VetCore, University of Veterinary Medicine uses Amira Software

      "Research at Vetmeduni Vienna is quite diverse, covering both clinical and preclinical research areas. We are currently four people working in the imaging facility, providing equipment and supports for researchers in both image acquisition (widefield microscopy, CLSM, spinning disk confocal microscopy, soon also STORM super-resolution microscopy, microscopic X-ray computed tomography) and in data visualization and analysis. Amira Software allows you to build networks, enabling complex interactions between data objects. Biology is also complex, and biological interactions are complex networks. Complex questions require complex tools to address them. In this respect, analysis networks such as used in Amira Software outperform most other software approaches when it comes to complex data analysis. Furthermore, I like that Amira Software is quite open concerning integration of deep learning networks and scripting (Tcl, Matlab, Python,...)."

      Stephan Handschuh, PhD
      VetCore, University of Veterinary Medicine, Vienna

       

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        EMBL and DKFZ uses Amira Software

        The present testimonial highlights the way Amira Software supported Matthia A. Karreman, MSc, PhD at EMBL and DKFZ, Heidelberg, Germany, in her project on multimodal correlative microscopy to efficiently target single tumor cells in vivo. Read reference paper.
        Video: 6 min

        Features

        Import and process imaging data

        Import and process your imaging data

          • Handle any modality, at any scale, of any size:

          - Bio-Formats
          - Bitmap formats
          - Microscopy: electron and optical
          - Medical and neuroimage formats
          - Molecular formats
          - Other acquisition devices (MRI, radiography, etc.)

          • Finite element modeling, geometric modeling, CAD
          • Support for multi-data/multi-view, multi-channel, time series, very large data
          • Scaling, calibration, conversion, re-sampling
          • Image enhancement, comprehensive filtering and convolution, Fourier frequency transforms
          • Artifact reduction algorithms
          • Advanced multi-mode 2D/3D automatic registration
          • Image stack alignment, arithmetic, correlation, fusion
          Segmentation

          Easily segment your imaging data

          • Thresholding and auto-segmentation, object separation, automatic labeling
          • Region growing, snakes, interpolation, wrapping, smoothing
          • Morphological processing, including watershed and basins
          • Machine Learning-based segmentation
          • Automatic tracing of individual fibers and filaments
          • Skeletonization and filament network extraction
          • Interactive tools for generation or editing of segmentation and spatial graphs
          • 3D surface reconstruction
          • Grid generation for FEA/CFD

           

          Presentation

          Export your analysis and visualization work to seamlessly publish and present it

          • Animation and video generation
          • Advanced key frame and object animation
          • Mix images, geometric models, measurements and simulations
          • Annotations, measures legends, histograms and curve plots
          • Export spreadsheets, 3D models, high-quality images
          • Active and passive 3D stereo vision
          • Single and tiled screen display
          • Immersive environment
          Visualize and explore

          Visualize and explore your imaging data

          • Interactive high-quality volume and multichannel visualization
          • Orthogonal, oblique, cylindrical and curved slicing
          • Contouring and iso-surface extraction
          • Maximum Intensity or other types of projections
          • Vector and tensor visualization
          • Objects and tracks
          • Molecular visualization
          Analysis and quantification

          Analyze your imaging data and obtain quantitative information

          • Intuitive recipe creation, customization, automated replay
          • Built-in measurements, including counts, volumes, areas, perimeters, aspect ratios and orientations
          • User-defined measures
          • Results viewer with spreadsheet tool and charting
          • Automatic individual feature measurements, 3D localization and spreadsheet selection
          • Automated statistics, distribution graphs
          • Feature filtering using any measurement criterion
          • Data registration, deformation, comparison and measurements

           

          Customization

          Easily and quickly adapt Amira Software to your specific needs

          • Custom C++ modules development
          • MATLAB™ bridge
          • Python scripting API
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          Products

          Thermo Scientific Amira 2D-5D visualization Software

          Amira Software
          Life Sciences

          • Explore 2D-5D bioimaging data
          • Identify and understand structures
          • Obtain statistical information
          • Share reports and stunning animations

           Download datasheet

          Thermo Scientific Krios G4 Cryo transmission electron microscope (TEM)

          Krios G4 Cryo-TEM

          • Improved ergonomics
          • Fits more easily into new and existing labs
          • Maximized productivity and automation
          • Best image quality for high-resolution 3D reconstruction

           Download datasheet

          Thermo Scientific Aquilos 2 cryo focused ion beam (FIB)

          Aquilos 2 Cryo-FIB

          • Automation enables production of multiple lamellas
          • Target and extract your structure of interest with lift-out nano-manipulator
          • 3D visualization for high-resolution tomography

           Download datasheet

          Thermo Scientific Apreo 2 scanning electron microscope (SEM)

          Apreo 2 SEM

          • High-performance SEM for all-round nanometer or sub-nanometer resolution
          • In-column T1 backscatter detector for sensitive, TV-rate materials contrast
          • Excellent performance at long working distance (10 mm)

           Download datasheet

          Contact us

          For Research Use Only. Not for use in diagnostic procedures.

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